Entamoeba histolytica has been separated into two species on the basis of molecular evidence obtained through 'riboprinting,' a technique devised in this laboratory, and on the basis of biochemical and immunological evidence obtained elsewhere. The name E. histolytica Schaudinn, 1903 has been retained for the invasive species, and E. dispar Brumpt, 1925 has been assigned to the noninvasive one. The first method to positively identify individual isolates of E. histolytica has been devised. The technology involved is based on the discovery of extensive polymorphism in two of the parasite's genes, one encoding a surface antigen, the other of unknown function. The method permits addressing important questions such as: Is there more than one strain circulating in the population? Are some strains more accountable than others for invasive disease? Do individual strains have tropisms for specific organs? The isolate identification method has provided evidence that in each of three published accounts of 'conversions' of E. dispar to E. histolytica, the 'conversions' resulted from cross-contamination of the E. dispar cultures with reference strains of E. histolytica present in the laboratories at the time those experiments were conducted. A second mitochondrion-specific gene has been identified in E. histolytica. This implies that other components of the protein importation apparatus will also be present. The existence of this organelle, possibly vestigial, has significant implications for the metabolism of drugs used to treat the infection as well as offering the potential for rational drug design. Taxonomic studies of the genus Entamoeba indicate profound divergence within the genus between species that develop cysts with different numbers of nucleic.